Change in the structure of fish assemblages was examined across the 100 km north-south stretch of the Houtman Abrolhos Islands, Western Australia and related to the southward flowing warm Leeuwin Current. Assemblages to the north at Ningaloo Reef and to the south at Rottnest Island were also compared to Houtman Abrolhos assemblages with reference to the Leeuwin current. Fish data was collected at all locations using baited remote underwater stereo-video systems (stereo-BRUVS) in depths of 8-12 m. 105 fish species were surveyed at the Houtman Abrolhos Islands during this study, 21% of these species have a warm-temperate latitudinal distribution, 13% sub-tropical and 66% tropical. Fish assemblages surveyed at the Houtman Abrolhos were distinct from, and somewhat intermediate between, fish assemblages surveyed to the south at Rottnest Island and to the north at Ningaloo. The composition of fish assemblages differed greatly across the four island groups of the Houtman Abrolhos and between sites within each group. While the Houtman Abrolhos fish assemblage is strongly Influenced by the Leeuwin current, large small-scale variability in assemblages within and across island groups is likely driven by non-exclusive factors such as the patchiness or complexity of the habitat, predator/prey relationships and competition.